The Ecuadorian Amazon, one of the richest reserves of biodiversity in the world, has faced one of the highest rates of deforestation of any Amazonian nation. Most of this forest elimination has been caused by agricultural colonization that followed the discovery of oil fields in 1967. Since the 1990s, an increasing process of urbanization has also engendered new patterns of population mobility within the Amazon, along with traditional ways by which rural settlers make their living. However, while very significant in its effects on deforestation, urbanization and regional development, population mobility within the Amazon has hardly been studied at all, as well as the distinct migration patterns between men and women. This paper uses a longitudinal dataset of 250 farm households in the Northern Ecuadorian Amazon to understand differentials between men and women migrants to urban and rural destinations and between men and women non-migrants. First, we use hazard analysis based on the Kaplan–Meier (KM) estimator to obtain the cumulative probability that an individual living in the study area in 1990 or at time t, will out-migrated at some time, t+n, before 1999. Results indicate that out-migration to other rural areas in the Amazon, especially pristine areas is considerably greater than out-migration to the growing, but still incipient, Amazonian urban areas. Furthermore, men are more likely to out-migrate to rural areas than women, while the reverse occurs for urban areas. Difference-of-means tests were employed to examine potential factors accounting for differentials between male and female out-migration to urban and rural areas. Among the key results, relative to men younger women are more likely to out-migrate to urban areas; more difficult access from farms to towns and roads constrains women’s migration; and access to new lands in the Amazon–an important cause of further deforestation–is more associated with male out-migration. Economic factors such as engagement in on-farm work, increasing resource scarcity–measured by higher population density at the farm and reduction in farm land on forest and crops–and increase in pasture land are more associated with male out-migration to rural areas. On the other hand, increasing resource scarcity, higher population density and weaker migration networks are more associated with female out-migration to urban areas. Thus, a vicious cycle is created: Pressure over land leads to deforestation in most or all farm forest areas and reduces the possibilities for further agricultural extensification (deforestation); out-migration, especially male out-migration, occurs to other rural or forest areas in the Amazon (with women being more likely to choose urban destinations); and, giving continuing population growth and pressures in the new settled areas, new pressures promote further out-migration to rural destinations and unabated deforestation.